I have been fighting with this for a while now, so I decided to scream for
help...

I have a ligand (segname P3) in a pocket (segname P1), and want to draw the
hydrogen bonds between them. To do this I tried selecting the Os from one
and the Ns from the other and then backwards (This is an all atom
structure, so it includes Hs). One of such selections would read

(segname P1 and name "O.*" and within 4 of segname P3) or (segname P3 and
name "N.*" and within 4 of segname P1)

if I use CPK representation, the selected atoms look right. Now, If I use
HBonds representation (4 Amstrongs, 40 degrees), it draws some good ones,
but it also draws some between Os in P1 and random Hs around.